Tzou W S, Hwang M J
Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC.
Biophys J. 1999 Sep;77(3):1191-205. doi: 10.1016/S0006-3495(99)76971-7.
A crucial element of many gene functions is protein-induced DNA bending. Computer-generated models of such bending have generally been derived by using a presumed bending angle for DNA. Here we describe a knowledge-based docking strategy for modeling the structure of bent DNA recognized by a major groove-inserting alpha-helix of proteins with a helix-turn-helix (HTH) motif. The method encompasses a series of molecular mechanics and dynamics simulations and incorporates two experimentally derived distance restraints: one between the recognition helix and DNA, the other between respective sites of protein and DNA involved in chemical modification-enabled nuclease scissions. During simulation, a DNA initially placed at a distance was "steered" by these restraints to dock with the binding protein and bends. Three prototype systems of dimerized HTH DNA binding were examined: the catabolite gene activator protein (CAP), the phage 434 repressor (Rep), and the factor for inversion stimulation (Fis). For CAP-DNA and Rep-DNA, the root mean square differences between model and x-ray structures in nonhydrogen atoms of the DNA core domain were 2.5 A and 1.6 A, respectively. An experimental structure of Fis-DNA is not yet available, but the predicted asymmetrical bending and the bending angle agree with results from a recent biochemical analysis.
许多基因功能的一个关键要素是蛋白质诱导的DNA弯曲。此类弯曲的计算机生成模型通常是通过使用假定的DNA弯曲角度推导出来的。在这里，我们描述了一种基于知识的对接策略，用于模拟由具有螺旋-转角-螺旋（HTH）基序的蛋白质的大沟插入α-螺旋识别的弯曲DNA的结构。该方法包括一系列分子力学和动力学模拟，并纳入了两个实验得出的距离限制：一个是识别螺旋与DNA之间的距离限制，另一个是蛋白质和DNA各自参与化学修饰激活的核酸酶切割的位点之间的距离限制。在模拟过程中，最初放置在一定距离处的DNA通过这些限制被“引导”与结合蛋白对接并弯曲。研究了二聚化HTH DNA结合的三个原型系统：分解代谢基因激活蛋白（CAP）、噬菌体434阻遏蛋白（Rep）和倒位刺激因子（Fis）。对于CAP-DNA和Rep-DNA，DNA核心结构域非氢原子的模型与X射线结构之间的均方根差异分别为2.5 Å和1.6 Å。Fis-DNA的实验结构尚未获得，但预测的不对称弯曲和弯曲角度与最近的生化分析结果一致。
